Definitely provide a sample or two; EXIF data will help also. It's way too hard to diagnose without seeing the results. Also, the focusing modes in effect will help a lot.
One thing you can do yourself is to take one of the original files out of the camera and load it into ViewNX2 - and then ask it to show the focus sensor that was locked on. You may get some surprises, especially if you've got one of the more advanced AF modes selected. A common mistake is to have dynamic area 51-point selected, which will give the AF system full license to pick any of the available AF sensors to lock on! For this reason I usually use single point, mostly so I know which AF sensor is being used.
_____ Brian... a bicoastal Nikonian and Team Member
My gallery is online. Comments and critique welcomed any time!